![FMODB](./images/FMODB-Logo_20190201-0_300ppi.png)
FMODB ID: QVZ1Y
Calculation Name: 4MBQ-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4MBQ
Chain ID: B
UniProt ID: Q9HZA6
Base Structure: X-ray
Registration Date: 2023-09-23
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 2.20220422 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 50 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -234754.299168 |
---|---|
FMO2-HF: Nuclear repulsion | 215595.144544 |
FMO2-HF: Total energy | -19159.154624 |
FMO2-MP2: Total energy | -19214.828598 |
3D Structure
Ligand structure
![ligand structure](./Kdata/F036629/ligand_interaction/ligand_F036629.png)
Ligand Interaction
![ligand interaction](./Kdata/F036629/ligand_interaction/ligand_interaction_F036629.png)
Ligand binding energy
"IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
---|---|---|---|---|---|
IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
N/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(B:869:GLY)
Summations of interaction energy for
fragment #1(B:869:GLY)
IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
---|---|---|---|---|---|
IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
-24.741 | -22.38 | 11.399 | -7.792 | -5.968 | -0.059 |
Interaction energy analysis for fragmet #1(B:869:GLY)
frag_NumFragment number. | ChainChain species. | Res #Residue number. | RES3-letter code of amino acid residue, ligand and solvent molecule. | FCHARGEFormal charge [e]. | q_MullikenFragment charge evaluated by Mulliken charge [e]. | q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. | DISTDistance from Ligand [Å]. | TotalIFIE at MP2 level [kcal/mol]. | ESElectro static interaction energy by PIEDA [kcal/mol]. | EXExchange-repulsion energy by PIEDA [kcal/mol]. | CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. | DI(MP2)Dispersion energy by PIEDA [kcal/mol]. | q(I=>J)Charge transfer value from I to J fragmens [e]. |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3 | B | 871 | ASP | -1 | -0.921 | -0.946 | 3.118 | -2.248 | 0.513 | 0.104 | -1.511 | -1.355 | 0.011 |
4 | B | 872 | GLU | -1 | -0.850 | -0.928 | 1.851 | -19.621 | -20.339 | 11.298 | -6.213 | -4.367 | -0.070 |
5 | B | 873 | ALA | 0 | 0.040 | 0.022 | 4.360 | 0.531 | 0.709 | -0.001 | -0.041 | -0.136 | 0.000 |
6 | B | 874 | ALA | 0 | -0.021 | -0.019 | 6.335 | 0.420 | 0.420 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | B | 875 | THR | 0 | 0.000 | 0.004 | 7.442 | 0.066 | 0.066 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | B | 876 | LYS | 1 | 0.823 | 0.902 | 7.047 | 2.023 | 2.023 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 877 | LEU | 0 | -0.006 | 0.005 | 10.256 | 0.122 | 0.122 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 878 | ASP | -1 | -0.888 | -0.936 | 12.239 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 879 | LEU | 0 | -0.039 | -0.019 | 12.137 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 880 | ALA | 0 | 0.024 | 0.016 | 14.281 | 0.037 | 0.037 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 881 | ARG | 1 | 0.808 | 0.876 | 14.295 | 0.166 | 0.166 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 882 | ALA | 0 | 0.019 | 0.016 | 17.677 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 883 | TYR | 0 | -0.039 | -0.019 | 17.047 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 884 | ILE | 0 | -0.022 | -0.005 | 19.615 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 885 | ASP | -1 | -0.945 | -0.964 | 22.285 | -0.084 | -0.084 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 886 | MET | 0 | -0.132 | -0.051 | 21.015 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 887 | GLY | 0 | -0.048 | -0.017 | 25.154 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 888 | ASP | -1 | -0.941 | -0.970 | 22.820 | -0.215 | -0.215 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 889 | SER | 0 | 0.013 | -0.018 | 22.226 | -0.021 | -0.021 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 890 | GLU | -1 | -0.846 | -0.918 | 21.525 | -0.224 | -0.224 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 891 | GLY | 0 | 0.054 | 0.030 | 19.873 | -0.026 | -0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 892 | ALA | 0 | -0.012 | -0.016 | 17.734 | -0.048 | -0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 893 | ARG | 1 | 0.812 | 0.888 | 16.690 | 0.165 | 0.165 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | B | 894 | ASP | -1 | -0.892 | -0.933 | 16.484 | -0.391 | -0.391 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | B | 895 | ILE | 0 | -0.011 | 0.001 | 12.243 | -0.080 | -0.080 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | B | 896 | LEU | 0 | -0.037 | -0.033 | 11.934 | -0.138 | -0.138 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | B | 897 | ASP | -1 | -0.952 | -0.972 | 12.676 | -0.574 | -0.574 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | B | 898 | GLU | -1 | -0.895 | -0.946 | 9.183 | -1.065 | -1.065 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | B | 899 | VAL | 0 | -0.022 | -0.014 | 8.124 | -0.260 | -0.260 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | B | 900 | LEU | 0 | -0.078 | -0.031 | 8.627 | -0.064 | -0.064 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | B | 901 | ALA | 0 | -0.016 | 0.008 | 9.287 | 0.102 | 0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | B | 902 | GLU | -1 | -0.893 | -0.930 | 4.059 | -2.722 | -2.652 | -0.001 | -0.012 | -0.057 | 0.000 |
35 | B | 903 | GLY | 0 | -0.017 | -0.008 | 4.461 | -0.645 | -0.575 | -0.001 | -0.015 | -0.053 | 0.000 |
36 | B | 904 | ASN | 0 | -0.036 | -0.019 | 6.592 | 0.208 | 0.208 | 0.000 | 0.000 | 0.000 | 0.000 |
37 | B | 905 | ASP | -1 | -0.830 | -0.934 | 8.044 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
38 | B | 906 | SER | 0 | -0.083 | -0.047 | 11.503 | 0.004 | 0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
39 | B | 907 | GLN | 0 | -0.014 | -0.023 | 6.379 | -0.375 | -0.375 | 0.000 | 0.000 | 0.000 | 0.000 |
40 | B | 908 | GLN | 0 | -0.026 | -0.018 | 9.981 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
41 | B | 909 | ALA | 0 | -0.063 | -0.035 | 12.100 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
42 | B | 910 | GLU | -1 | -0.800 | -0.893 | 13.712 | -0.123 | -0.123 | 0.000 | 0.000 | 0.000 | 0.000 |
43 | B | 911 | ALA | 0 | 0.016 | 0.007 | 12.657 | 0.010 | 0.010 | 0.000 | 0.000 | 0.000 | 0.000 |
44 | B | 912 | ARG | 1 | 0.938 | 0.960 | 14.733 | 0.277 | 0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
45 | B | 913 | GLU | -1 | -0.814 | -0.881 | 17.536 | -0.102 | -0.102 | 0.000 | 0.000 | 0.000 | 0.000 |
46 | B | 914 | LEU | 0 | 0.008 | -0.006 | 15.940 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
47 | B | 915 | LEU | 0 | -0.043 | -0.030 | 16.407 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
48 | B | 916 | GLU | -1 | -1.016 | -1.000 | 20.070 | -0.126 | -0.126 | 0.000 | 0.000 | 0.000 | 0.000 |
49 | B | 917 | ARG | 1 | 0.763 | 0.888 | 21.350 | 0.136 | 0.136 | 0.000 | 0.000 | 0.000 | 0.000 |
50 | B | 918 | LEU | 0 | -0.071 | -0.027 | 20.615 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |